[gmx-users] precision of input gro file

[Yu Ogawa]

Hi Mark,
Thanks for suggestions. I will take a look at the g96 format.
I try to deform a part of polymer crystal with a small displacement, and
then relax the structure in MD while keeping the displacement by
constraint. As the displacement can be very small, I want to have an input
structure file with a higher precision.
Thanks!
Yu

2017-06-15 13:12 GMT+01:00 Mark Abraham <mark.j.abraham at gmail.com>:

> Hi,
>
> Usually one doesn't need a higher precision text file. The g96 format does
> work for this, but you should probably be using a real trajectory or
> checkpoint format for whatever you are trying to do. That would have been
> good to describe, rather than assuming the form of the solution ;-)
>
> Mark
>
> On Thu, 15 Jun 2017 13:10 Yu Ogawa <ayogwa at gmail.com> wrote:
>
> > Hi Eric,
> > Thanks for replying.
> >
> > I may be wrong, but what I understand from the online manual is that we
> > have a higher precision in MD calculation (as in trr file). I am not sure
> > if grompp recognizes a higher precision than 3 decimal places.
> >
> > When I did editconf with a gro file with higher precision as an input, I
> > got an output gro file with coordinates rounded to 3 decimal places. So I
> > am a bit doubtful if it's the case with the grompp program.
> >
> >
> > 2017-06-15 11:49 GMT+01:00 Eric Smoll <ericsmoll at gmail.com>:
> >
> > > Hello Yu,
> > >
> > > Read this carefully.
> > >
> > > http://manual.gromacs.org/online/gro.html
> > >
> > > As far as I know, Gromacs will accept gro files with high precision if
> > the
> > > input file follows this format.
> > >
> > > Best,
> > > Eric
> > >
> > > > On Jun 15, 2017, at 4:33 AM, Yu Ogawa <ayogwa at gmail.com> wrote:
> > > >
> > > > Hello gmx users,
> > > > Can we increase a precision of input structure file more than 3
> decimal
> > > > places?
> > > > Thank you for your help!
> > > > Yu
> > > > --
> > > > Gromacs Users mailing list
> > > >
> > > > * Please search the archive at http://www.gromacs.org/
> > > Support/Mailing_Lists/GMX-Users_List before posting!
> > > >
> > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > >
> > > > * For (un)subscribe requests visit
> > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> > > send a mail to gmx-users-request at gromacs.org.
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at http://www.gromacs.org/
> > > Support/Mailing_Lists/GMX-Users_List before posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-request at gromacs.org.
> > >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>